CRISPR-StAR, a paradigm leveraging internal controls, empowers genetic screening in vivo (batch 2)

Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo. Overall design: To investigate the in vivo-specific dependencies in melanoma, we performed a genome-wide CRISPR/Cas9 screen, as well as smaller validation screens. The samples obtained from the screened in vivo tumors and in vitro cells were processed with NGS. And subsequently analysed using Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK). However, we performed analysis according the CRISPR-StAR analysis method. Genome-wide screen was performed in 2 batches.